Focused 100-plex HDI-STARR-seq library in mouse liver
HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivoA focused STARR-seq plasmid library targeted 100 mouse liver DNase-I hypersensitive regions, with 100 successfully cloned genomic PCR targets and additional measurable MACS2 subpeaks. The STARR-TYC3/7 library was delivered to vehicle-treated male and female mice and TCPOBOP-treated male mice by hydrodynamic tail-vein injection; liver reporter RNA and DNA were collected 7 days after delivery.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Vehicle (corn oil) or TCPOBOP (3 mg/kg, 1 day before collection); control male versus control female liver
Episomal STARR-seq plasmid delivery by hydrodynamic injection. Reporter inserts were cloned downstream of a modified 318-nt minimal mouse Albumin promoter and are transcribed in the reporter RNA; activity is the normalized RNA/DNA ratio for the same liver condition. The focused plasmid pool was a 1:1 weight mixture of STARR-TYC3 and STARR-TYC7 libraries.
Processed data
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 50 definitions
- element_id
- Unique focused-library MACS2 peak identifier.
- chromosome
- Mouse mm9 chromosome.
- start_mm9
- Reported mm9 genomic start coordinate.
- end_mm9
- Reported mm9 genomic end coordinate.
- width_bp
- Peak width in base pairs (end minus start).
- genomic_pcr_id
- Identifier of the original genomic PCR target, when applicable.
- in_gPCR_target
- Indicator that the peak overlaps one of the 100 genomic PCR targets (1=yes, 0=no).
- rna_raw_tcpo_male_rep1
- Raw reporter-RNA read count for TCPOBOP-treated male liver replicate 1.
- rna_raw_tcpo_male_rep2
- Raw reporter-RNA read count for TCPOBOP-treated male liver replicate 2.
- rna_raw_vehicle_male_rep1
- Raw reporter-RNA read count for vehicle-treated male liver replicate 1.
- rna_raw_vehicle_male_rep2
- Raw reporter-RNA read count for vehicle-treated male liver replicate 2.
- rna_raw_vehicle_female_rep1
- Raw reporter-RNA read count for vehicle-treated female liver replicate 1.
- rna_raw_vehicle_female_rep2
- Raw reporter-RNA read count for vehicle-treated female liver replicate 2.
- rna_raw_vehicle_female_rep3
- Raw reporter-RNA read count for vehicle-treated female liver replicate 3.
- rna_raw_vehicle_female_rep4
- Raw reporter-RNA read count for vehicle-treated female liver replicate 4.
- dna_raw_tcpo_male
- Raw liver-extracted DNA library read count for the TCPOBOP-treated male condition.
- dna_raw_vehicle_male
- Raw liver-extracted DNA library read count for the vehicle-treated male condition.
- dna_raw_vehicle_female
- Raw liver-extracted DNA library read count for the vehicle-treated female condition.
- dna_raw_input_plasmid
- Raw read count in the original focused plasmid library.
- rna_norm_tcpo_male_rep1
- Reporter-RNA reads normalized per 10 million mapped reads for TCPOBOP male replicate 1.
- rna_norm_tcpo_male_rep2
- Reporter-RNA reads normalized per 10 million mapped reads for TCPOBOP male replicate 2.
- rna_norm_vehicle_male_rep1
- Reporter-RNA reads normalized per 10 million mapped reads for vehicle male replicate 1.
- rna_norm_vehicle_male_rep2
- Reporter-RNA reads normalized per 10 million mapped reads for vehicle male replicate 2.
- rna_norm_vehicle_female_rep1
- Reporter-RNA reads normalized per 10 million mapped reads for vehicle female replicate 1.
- rna_norm_vehicle_female_rep2
- Reporter-RNA reads normalized per 10 million mapped reads for vehicle female replicate 2.
- rna_norm_vehicle_female_rep3
- Reporter-RNA reads normalized per 10 million mapped reads for vehicle female replicate 3.
- rna_norm_vehicle_female_rep4
- Reporter-RNA reads normalized per 10 million mapped reads for vehicle female replicate 4.
- dna_norm_tcpo_male
- TCPOBOP male DNA-library reads normalized per 10 million mapped reads.
- dna_norm_vehicle_male
- Vehicle male DNA-library reads normalized per 10 million mapped reads.
- dna_norm_vehicle_female
- Vehicle female DNA-library reads normalized per 10 million mapped reads.
- dna_norm_input_plasmid
- Input plasmid-library reads normalized per 10 million mapped reads.
- activity_tcpo_male_rep1
- Per-replicate normalized RNA/DNA enhancer activity for TCPOBOP male replicate 1.
- activity_tcpo_male_rep2
- Per-replicate normalized RNA/DNA enhancer activity for TCPOBOP male replicate 2.
- activity_vehicle_male_rep1
- Per-replicate normalized RNA/DNA enhancer activity for vehicle male replicate 1.
- activity_vehicle_male_rep2
- Per-replicate normalized RNA/DNA enhancer activity for vehicle male replicate 2.
- activity_vehicle_female_rep1
- Per-replicate normalized RNA/DNA enhancer activity for vehicle female replicate 1.
- activity_vehicle_female_rep2
- Per-replicate normalized RNA/DNA enhancer activity for vehicle female replicate 2.
- activity_vehicle_female_rep3
- Per-replicate normalized RNA/DNA enhancer activity for vehicle female replicate 3.
- activity_vehicle_female_rep4
- Per-replicate normalized RNA/DNA enhancer activity for vehicle female replicate 4.
- activity_mean_tcpo_male
- Source mean enhancer activity for the TCPOBOP-treated male group.
- activity_mean_vehicle_male
- Source mean enhancer activity for the vehicle-treated male group.
- activity_mean_vehicle_female
- Source mean enhancer activity for the vehicle-treated female group.
- tcpo_vs_vehicle_male_log2fc
- Derived log2 fold change of mean TCPOBOP-male activity divided by vehicle-male activity; NA when either mean is nonpositive or missing.
- female_vs_vehicle_male_log2fc
- Derived log2 fold change of mean vehicle-female activity divided by vehicle-male activity; NA when either mean is nonpositive or missing.
- tcpo_pvalue
- Unpaired Student t-test p-value for TCPOBOP-treated male versus vehicle-treated male activity, available for the annotated targeted regions.
- tcpo_stringent_flag
- Source indicator for p-value below 0.05 in the TCPOBOP versus male-control comparison.
- tcpo_activity_category
- Source condition-response category for TCPOBOP-responsive targeted regions.
- sex_pvalue
- Unpaired Student t-test p-value for vehicle-treated female versus vehicle-treated male activity, available for the annotated targeted regions.
- sex_stringent_flag
- Source indicator for p-value below 0.05 in the female versus male comparison.
- sex_activity_category
- Source sex-bias category for targeted regions.
Quality control
The authors aligned paired-end reads to mm9 with Bowtie2, retained uniquely aligned reads, called and merged MACS2 peaks across plasmid, liver-DNA and reporter-RNA libraries, and removed ENCODE-blacklisted or PCR-duplicate-only peaks. The source focused table contains 1,673 merged peak regions. For this packaged table, entries were additionally required to have valid mm9 coordinates and at least one nonzero DNA/input-plasmid count; 33 regions with zero across all four DNA/plasmid columns were removed, leaving 1,640 rows. Non-finite RNA/DNA ratios from zero denominators are represented as NA.
Curation notes
The focused union contains the 100 intended gPCR regions plus 1,573 nonspecific PCR-amplification subpeaks described by the authors; all measurable union peaks are retained. Focused RNA replicates are n=2 TCPOBOP male, n=2 vehicle male and n=4 vehicle female; DNA libraries are one per condition plus the input plasmid. Targeted p-values/categories are unavailable for most nonspecific subpeaks and are left as NA.